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- EMDB-6624: HIV-1 CSL envelope glycoprotein trimer bound to bnAb PGV04 -

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Basic information

Entry
Database: EMDB / ID: EMD-6624
TitleHIV-1 CSL envelope glycoprotein trimer bound to bnAb PGV04
Map dataHIV-1 CSL envelope glycoprotein trimer bound to bnAb PGV04
Sample
  • Sample: HIV-1 CSL envelope glycoprotein trimer bound to PGV04
  • Protein or peptide: CSL
  • Protein or peptide: bnAb PGV04
KeywordsHIV / Envelope / glycoprotein / trimer
Biological speciesHuman immunodeficiency virus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsKong L / He L / de Val N / Morris CD / Vora N / Azadnia P / Sok D / Zhou B / Burton DR / Ward AB ...Kong L / He L / de Val N / Morris CD / Vora N / Azadnia P / Sok D / Zhou B / Burton DR / Ward AB / Wilson IA / Zhu J
CitationJournal: Nat Commun / Year: 2016
Title: Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability.
Authors: Leopold Kong / Linling He / Natalia de Val / Nemil Vora / Charles D Morris / Parisa Azadnia / Devin Sok / Bin Zhou / Dennis R Burton / Andrew B Ward / Ian A Wilson / Jiang Zhu /
Abstract: The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. ...The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains.
History
DepositionMar 17, 2016-
Header (metadata) releaseMay 11, 2016-
Map releaseJul 13, 2016-
UpdateJul 20, 2016-
Current statusJul 20, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 25.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 25.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6624.tif

Downloads & links

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Map

FileDownload / File: emd_6624.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 CSL envelope glycoprotein trimer bound to bnAb PGV04
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 25.600000000000001 / Movie #1: 25.6
Minimum - Maximum-101.675537109999993 - 139.898178099999996
Average (Standard dev.)0.45218727 (±9.46966362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-101.676139.8980.452

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Supplemental data

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Sample components

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Entire : HIV-1 CSL envelope glycoprotein trimer bound to PGV04

EntireName: HIV-1 CSL envelope glycoprotein trimer bound to PGV04
Components
  • Sample: HIV-1 CSL envelope glycoprotein trimer bound to PGV04
  • Protein or peptide: CSL
  • Protein or peptide: bnAb PGV04

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Supramolecule #1000: HIV-1 CSL envelope glycoprotein trimer bound to PGV04

SupramoleculeName: HIV-1 CSL envelope glycoprotein trimer bound to PGV04 / type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 2
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: CSL

MacromoleculeName: CSL / type: protein_or_peptide / ID: 1
Details: Heterodimer of gp120 and gp41 assembles into a trimer.
Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus / synonym: HIV
Molecular weightTheoretical: 420 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #2: bnAb PGV04

MacromoleculeName: bnAb PGV04 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightTheoretical: 50 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris-HCl, 150 mM NaCl
StainingType: NEGATIVE
Details: Grids were glow discharged at 20 mA for 30 seconds, then stained for 40 seconds using 2% uranyl formate.
GridDetails: 400 Cu mesh grids
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
DateOct 23, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 111 / Average electron dose: 30.18 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 46000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN2, sparx / Number images used: 12473
Final two d classificationNumber classes: 112

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